Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
USF1

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
antibody antibodydescription
Rabbit polyclonal, USF-1 (C-20). Antibody Target: USF1
antibody targetdescription
The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.
antibody vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-229
protocol description
a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
controlid
SL217,SL218
labexpid
SL448,SL483
labversion
PCR2x
labversion description
a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
replicate
1,2
softwareversion
MACS
antibody vendorid
sc-229
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR2x
protocol description
2-cycles of PCR (Myers)
controlid
SL217
labexpid
SL448
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803347: HudsonAlpha_ChipSeq_GM12878_USF-1_PCR2x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
58662101
Reads aligned (%)
43.9
Duplicates removed (%)
14.4
Number of peaks
9804 (qval < 1E-05)

hg38

Number of total reads
58662101
Reads aligned (%)
45.1
Duplicates removed (%)
20.2
Number of peaks
9378 (qval < 1E-05)

Base call quality data from DBCLS SRA